Francis made his comments in an impromptu response to a question at a meeting of the small Catholic community in the ex-Soviet republic of Georgia.
"You mentioned a great enemy of marriage: gender theory," the pope said in response to a woman who had asked about it being taught in schools.
He did not elaborate.
Gender theory is broadly the concept that while a person may be biologically male or female, they have the right to identify themselves as male, female, both or neither.
"Today, there is a global war out to destroy marriage," Francis said. "Not with weapons but with ideas ... we have to defend ourselves from ideological colonisation."
Francis, who has been more accepting of homosexuals than his predecessors but opposes gay marriage, also appeared to be referring to it when he said "marriage is the most beautiful thing that God has created" adding that the Bible says God created man and woman to become one flesh.
In the same answer, he said the growing acceptance of divorce was another threat to the family.
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